From OpenWetWare
Jump to navigationJump to search

<html> <script> function addStylesheet(url) {

   // presentation mode
   if (document.createStyleSheet) {
   else {
       var styles = "@import url('" + url +  "');";
       var newSS=document.createElement('link');

} if (location.href.indexOf('action=render') > 0) {

   document.write("<head><title>Presentation</title></head>"); // need this for some browsers for addStylesheet to work
   document.write('<script src="" type="text/javascript"><' + '/script>');
   document.write('<script type="text/javascript">wgBreakFrames = false;<' + '/script>'); // for wikibits.js
   document.write('<script src="/skins/common/wikibits.js" type="text/javascript"><' + '/script>');
   document.write('<script src="/index.php?title=-&action=raw&smaxage=0&gen=js" type="text/javascript"><' + '/script>');

} else {

   // wiki mode
   if (wgServer)
       document.write('<a href="' + wgServer + '/index.php?title=' + wgPageName + '&action=render"><b><em>=> Start web presentation</em></b></a>');

} </script> </html>


A wiki for capturing and sharing biological knowledge

Reshma P. Shetty and Jeremy Muhlich


Much of the knowledge produced by biological research is passed down by oral tradition.

This makes it difficult for newcomers to enter the field.

Solution: OpenWetWare

OpenWetWare's contributions

  1. Easy and collaborative content generation
  2. Community discourse

Labs on OpenWetWare

Integrating OpenWetWare into research

Examining Communication

Ethnomethodology: A sociological discipline which focuses on the ways in which people make sense of their world, display this understanding to others, and produce the mutually shared social order in which they live. (Wikipedia)

Discourse Analysis

Dysfunctionality of Model Publishing

figure: Ty Thomson

Systematization and Data Standards

<html><img src=""</img></html>

  • Standards for models
    • MIRIAM - Minimum Information Requested in the Annotation of Biochemical Models
    • SBML - Systems Biology Markup Language
  • Communicating with computers, not people
  • Rigid, one-way "conversation"

Literate Programming

Donald Knuth, 1981

Write programs primarily for humans, not computers

Ty Thomson, MIT

80-20 Rule / Pareto Principle

How do we communicate the final 20% ?

  • Verbal, email, etc.
  • Wiki

Conversation is robust, and necessary anyway

Agile Informatics effort

Wiki-based model documentation

with Brian Joughin, MIT/ICBP

To be integrated into OWW

Part of a larger workflow:

"Living" Models

OpenWetWare's success

  • 2,800 contributors
  • 100 labs
  • 1.5 million pageviews per month
  • 275,000 sessions per month